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  • 1
    Publication Date: 2010-11-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beloqui, Ana -- Guazzaroni, Maria Eugenia -- Pazos, Florencio -- Vieites, Jose M -- Godoy, Marta -- Golyshina, Olga V -- Chernikova, Tatyana N -- Waliczek, Agnes -- Silva-Rocha, Rafael -- Al-Ramahi, Yamal -- La Cono, Violetta -- Mendez, Carmen -- Salas, Jose A -- Solano, Roberto -- Yakimov, Michail M -- Timmis, Kenneth N -- Golyshin, Peter N -- Ferrer, Manuel -- New York, N.Y. -- Science. 2010 Nov 12;330(6006):912. doi: 10.1126/science.330.6006.912-a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21071648" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2009-10-10
    Description: We describe a sensitive metabolite array for genome sequence-independent functional analysis of metabolic phenotypes and networks, the reactomes, of cell populations and communities. The array includes 1676 dye-linked substrate compounds collectively representing central metabolic pathways of all forms of life. Application of cell extracts to the array leads to specific binding of enzymes to cognate substrates, transformation to products, and concomitant activation of the dye signals. Proof of principle was shown by reconstruction of the metabolic maps of model bacteria. Utility of the array for unsequenced organisms was demonstrated by reconstruction of the global metabolisms of three microbial communities derived from acidic volcanic pool, deep-sea brine lake, and hydrocarbon-polluted seawater. Enzymes of interest are captured on nanoparticles coated with cognate metabolites, sequenced, and their functions unequivocally established.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beloqui, Ana -- Guazzaroni, Maria-Eugenia -- Pazos, Florencio -- Vieites, Jose M -- Godoy, Marta -- Golyshina, Olga V -- Chernikova, Tatyana N -- Waliczek, Agnes -- Silva-Rocha, Rafael -- Al-Ramahi, Yamal -- La Cono, Violetta -- Mendez, Carmen -- Salas, Jose A -- Solano, Roberto -- Yakimov, Michail M -- Timmis, Kenneth N -- Golyshin, Peter N -- Ferrer, Manuel -- New York, N.Y. -- Science. 2009 Oct 9;326(5950):252-7. doi: 10.1126/science.1174094.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CSIC, Institute of Catalysis, 28049 Madrid, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19815770" target="_blank"〉PubMed〈/a〉
    Keywords: Archaea/genetics/metabolism ; Bacteria/genetics/*metabolism ; Bacterial Proteins/metabolism ; Computational Biology ; Ecosystem ; Enzymes/*metabolism ; Enzymes, Immobilized ; Genome, Archaeal ; *Genome, Bacterial ; Hot Springs/microbiology ; *Metabolic Networks and Pathways ; *Metabolome ; Metabolomics/*methods ; Microarray Analysis/*methods ; Nanoparticles ; Pseudomonas putida/genetics/metabolism ; Seawater/microbiology ; Streptomyces coelicolor/genetics/metabolism ; Water Microbiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2019
    Print ISSN: 1061-4036
    Electronic ISSN: 1546-1718
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 4
    Publication Date: 2019
    Print ISSN: 1061-4036
    Electronic ISSN: 1546-1718
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 5
    Publication Date: 2012-04-07
    Description: The impact of low-frequency climate modes on the large-scale variability of chlorophyll-a (a proxy for phytoplankton biomass) concentration in the subtropics is little known. Here we examined the concurrent monthly chlorophyll-a and hydrographical records obtained at two subtropical time series stations (Bermuda Atlantic Time series Study, BATS and European Station for Time series in the Ocean Canary Islands, ESTOC) from the beginning of the time series (1989 at BATS and 1994 at ESTOC) to 2003, in order to analyze its seasonal and interannual variability and investigate the potential correlation with large-scale atmospheric oscillations. At BATS, Chl-a variations are mainly caused by differences in the convective mixing and mesoscale phenomena. Variability in winter mixing is a significant factor at ESTOC as exemplified by years with anomalously deep mixed layer depths. An additional nutrient source causing Chl-a variability at this station likely occurs due to nutrient advection driven by the baroclinic flow caused by the Trade Winds during summertime. We found that interannual variability in mean integrated total Chl-a (TChl-a) is significantly correlated with temperature and salinity anomalies at BATS. Chl-a also covaried with changes in temperature although the correlation was not significant at ESTOC. We could not find any direct correlation between TChl-a and NAO at BATS; the correlation improved between TChl-a and NAO +1 year but was still insignificant. However, significant correlations were found for ESTOC between TChl-a anomalies and ENSO (El Niño Southern Oscillation) +3 years and NAO +1 year time lag.
    Print ISSN: 0886-6236
    Electronic ISSN: 1944-9224
    Topics: Biology , Chemistry and Pharmacology , Geography , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 6
    Publication Date: 2013-06-24
    Description: Motivation: Life Sciences have emerged as a key domain in the Linked Data community because of the diversity of data semantics and formats available through a great variety of databases and web technologies. Thus, it has been used as the perfect domain for applications in the web of data. Unfortunately, bioinformaticians are not exploiting the full potential of this already available technology, and experts in Life Sciences have real problems to discover, understand and devise how to take advantage of these interlinked (integrated) data. Results: In this article, we present Bioqueries, a wiki-based portal that is aimed at community building around biological Linked Data. This tool has been designed to aid bioinformaticians in developing SPARQL queries to access biological databases exposed as Linked Data, and also to help biologists gain a deeper insight into the potential use of this technology. This public space offers several services and a collaborative infrastructure to stimulate the consumption of biological Linked Data and, therefore, contribute to implementing the benefits of the web of data in this domain. Bioqueries currently contains 215 query entries grouped by database and theme, 230 registered users and 44 end points that contain biological Resource Description Framework information. Availability: The Bioqueries portal is freely accessible at http://bioqueries.uma.es . Contact: jfam@lcc.uma.es Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 7
    Publication Date: 2014-02-12
    Description: Transcription factors (TFs) regulate gene expression through binding to cis-regulatory specific sequences in the promoters of their target genes. In contrast to the genetic code, the transcriptional regulatory code is far from being deciphered and is determined by sequence specificity of TFs, combinatorial cooperation between TFs and chromatin competence. Here...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 8
    Publication Date: 2014-01-29
    Description: Motivation:  Molecular docking is a method for structure-based drug design and structural molecular biology, which attempts to predict the position and orientation of a small molecule (ligand) in relation to a protein (receptor) to produce a stable complex with a minimum binding energy. One of the most widely used software packages for this purpose is AutoDock, which incorporates three metaheuristic techniques. We propose the integration of AutoDock with jMetalCpp, an optimization framework, thereby providing both single- and multi-objective algorithms that can be used to effectively solve docking problems. Results:  The resulting combination of AutoDock + jMetalCpp allows users of the former to easily use the metaheuristics provided by the latter. In this way, biologists have at their disposal a richer set of optimization techniques than those already provided in AutoDock. Moreover, designers of metaheuristic techniques can use molecular docking for case studies, which can lead to more efficient algorithms oriented to solving the target problems. Availability and implementation:  jMetalCpp software adapted to AutoDock is freely available as a C++ source code at http://khaos.uma.es/AutodockjMetal/ . Contact:   jfam@lcc.uma.es Supplementary information:   Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 9
    ISSN: 1432-1955
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract We developed a method for avoiding contamination by fibroblasts when cultures of peritoneal cells are initiated. Macrophages were identified by immunogold detection [light microscope, transmission (TEM) and scanning (SEM) electron microscopes] of membrane antigens (Mac-1+, Thy-1,2−), non-specific esterase activity and ultrastructural features (TEM). As compared with controls, the yield of peritoneal macrophages was 2- and 12-fold higher, respectively, in acutely and chronically infected mice. In all, 30 “chronic”, 18 “acute” and 18 control cultures were followed up. At a given cell-density seeding, the decline of control, “acute” and “chronic” cultures starts at about day 10, 15, and 27, respectively. In “chronic” cultures only, fibroblast-like cells appear from day 6 onwards; their number increases with time. Cells showing characters intermediary between macrophages and fibroblasts were observed. We suggest that fibroblast-like cells result from the in vitro transdifferentiation of a limited number of in vivo committed macrophages.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1432-2056
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Serum and milk Immunoglobulin M (IgM) concentrations in 11 mother-pup pairs were measured in southern elephant seals (Mirounga leonina) throughout lactation during 2 breeding seasons at King George Island. Samples were obtained sequentially throughout the suckling period (approximately 23 days). The IgM concentration was measured by single radial immunodiffusion on agarose plates. Milk IgM concentrations showed significant differences throughout lactation, with the highest concentrations on the 1st day (x=989.7 mg/dL skimmed milk; SD=433.2) followed by a sharp fall during the next 3–6 days of the suckling period. The ratio of milk IgM/serum IgM concentrations from mothers ranged from 0.21 to 21.92, with highest values in the 1st day of lactation (x=8.25, SD=5.4) and a decrease in concentration as lactation progressed. This was due to the fact that, throughout lactation, milk IgM concentrations fell while serum IgM values showed an increasing trend. Pups showed the lowest serum IgM values in the 1st day of the suckling period (x=13.0 mg/dL, SD=4.3) with an increasing trend as lactation progressed. Despite the high IgM concentrations of milk at day 1 of lactation, by 1 week of age pups had serum IgM concentrations only slightly greater than at birth. This suggests that much of this Ig was newly formed and little or no milk IgM was absorbed during the 1st week. Possibly, the function of ingested IgM is to provide local immunity in the pup's gut, during the first few days of postnatal life.
    Type of Medium: Electronic Resource
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